Wikipedia talk:WikiProject Biology

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WikiProject Biology (Rated Project-class)
WikiProject iconWikiProject Biology is part of the WikiProject Biology, an effort to build a comprehensive and detailed guide to biology on Wikipedia.
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Epigenetics[edit]

This interrelated series of articles is one of the most disoriented, contradictory and factually compromised sets that I've encountered on our project in quite some time. Moreover, the overlapping nature of content and lack of adequately unambiguous central navigation is confusing, even for someone who has existing familiarity with the general topic. I'm not certain of how much available manpower WikiProject Biology has to offer at the moment, but I'd like to get the ball rolling on a collaborative effort of some sort.   — C M B J   04:56, 15 November 2011 (UTC)

A thorough review of the gene article[edit]

Transcluded from Talk:Gene/Review

To WP:MCB, WP:GEN, WP:BIOL and WP:EB

The gene article gets 50,000 views per month but has been de-listed as a featured article since 2006. Given the success of the recent blitz on the enzyme article, I thought I'd suggest spending a couple of weeks seeing if we can get it up to a higher standard. I'm going to start with updating some of the images. If you'd like to help out on the article, it'd be great to see you there. T.Shafee(Evo﹠Evo)talk 09:49, 31 March 2015 (UTC)

It appears the main reason gene was delisted as a GA was sourcing (see Talk:Gene/GA1). The following free textbook is probably sufficient to document most basic facts about genes:
  • Alberts B, Johnson A, Lewis J, Raff M, Roberts K, Walter P (2002). Molecular Biology of the Cell (Fourth ed.). New York: Garland Science. ISBN 978-0-8153-3218-3.
a second one is even more relevant, but unfortunately not freely accessed:
I will start working on this as I find time. Boghog (talk) 17:58, 31 March 2015 (UTC)
Thanks for the prompt on this! I see I did do some work here back in the day, but not enough. Looks like a typical large-but-untended wiki article - bloated up with random factoids with no attention to the flow of the article. I'm pretty busy for this week and out of town next week, but I'll try to give it some attention. Opabinia regalis (talk) 19:19, 31 March 2015 (UTC)
I'll probably go through and make all the necessary MOS tweaks for FA status to the article within the next week. Too preoccupied with other articles at the moment to make any substantive content/reference changes though. Seppi333 (Insert  | Maintained) 03:24, 1 April 2015 (UTC)

Glossary[edit]

Snooping around I encountered Template:Genetics glossary, I don't know it's backstory, but it is a rather cleaver idea for a template in my opinion. I partially reckon it might go well under the first image in place or the second image depicting DNA, which conceptually is a tangent. I am not sure, hence my asking. --Squidonius (talk) 21:47, 1 April 2015 (UTC)

Including a glossary could be useful, but I think it should be concise and tailored specifically for this article. Currently {{Genetics glossary}} contains 22 entries and some of the definitions are quite lengthy. A shorter glossary, closer to the size of {{Transcription factor glossary}} or {{Restriction enzyme glossary}}, IMHO would be more effective. Another option is to transclude the {{Genetics sidebar}} which in turn links to {{Genetics glossary}}. Boghog (talk) 06:38, 2 April 2015 (UTC)
...could also just transclude a collapsed version - provides the full set of terms and takes up little space. If people need a glossary, they can expand it. Glossaries probably shouldn't be expanded by default unless there's a lot of free space along the right side of the page between level 2 sections (i.e., horizontal line breaks), since images and tables should take precedence. Seppi333 (Insert  | Maintained) 07:25, 2 April 2015 (UTC)
Collapsed or not collapsed, {{Genetics glossary}} is still way too long. Glossaries should be restricted to key terms with short definitions that can quickly be scanned while reading the rest of the article. IMHO, a long glossary defeats its purpose. Furthermore an uncollapsed glossary is more likely be read and if kept short, no need to collapse. Boghog (talk) 08:30, 2 April 2015 (UTC)
Fair enough. Might as well make a new one since it's not referenced anyway; imo, glossaries should cite sources, preferably another glossary, because it's article content. Seppi333 (Insert  | Maintained) 08:39, 2 April 2015 (UTC)
Hmm, apparently I added a bunch of stuff to that template awhile back, but don't remember it at all. It appears to be a subset of the article genetics glossary. (I'm not really sure we need both.) I agree that the template is way too long, and as constructed is hard to ctrl-F for a term.
I suggest just linking to the MBC glossary as a "reference". I would consider this kind of thing as a summary analogous to the lead paragraphs; no need for a clutter of little blue numbers. Opabinia regalis (talk) 21:47, 2 April 2015 (UTC)

References[edit]

I'm planning on adding some more Molecular Biology of the Cell references to the article using {{rp}} to specify chapter sections. I went to the MBOC 4th ed. online page but I can find no way of searching by page number, chapter, section or anything else. Any ideas on how to specify specific sections as is possible for Biochemistry 5th ed. online? Alternatively, maybe there's a more easily refernced online textbook for general citations. T.Shafee(Evo﹠Evo)talk 11:30, 20 April 2015 (UTC)

I had the same train of thought here on the regular talk page. How about something like this? Uses {{sfn}} to include links to individual sections as notes. Of course, now they're separate from the rest of the references, but maybe it's not a bad idea to distinguish 'basic stuff you can find in a textbook' from 'specific results you need to consult the literature for'. Opabinia regalis (talk) 06:09, 21 April 2015 (UTC)
You're right, I missed that. I agree that it's actually a good way to format it. Having a separate list that indicates the significance of the references is useful. T.Shafee(Evo﹠Evo)talk 08:06, 21 April 2015 (UTC)
I am not a big fan of {{sfn}} templates. They are more complicated and harder to maintain. Plus they don't directly address the problem of searching Molecular Biology of the Cell. What seems to work is to search for the chapter or subchapter titles in quotes. For example search for "DNA and Chromosomes" provides a link to the introduction of chapter 4. Then one can reference the chapter or subchapter number with {{rp}}. I am busy this week but should have more time this weekend to work on this. Boghog (talk) 12:21, 21 April 2015 (UTC)
I mis-described my own suggestion; it's actually {{efn}} (not that that's better). I like your method better from an aesthetic and maintenance point of view, but the problem is that giving a reader a reference to "chapter 4" is less useful if there's no obvious way to get to chapter 4 from the book's table of contents page. I don't see a way to provide separate links for each chapter/section without splitting up the references in the reference list. We could use {{rp}} like this, but I think the links police won't like that. Opabinia regalis (talk) 18:03, 21 April 2015 (UTC)
OK, I now see what you mean. The choice is between {{efn}} and in-line external links and {{efn}} is the lesser of two evils. One other possibility is to append the chapter external links to the citation:
or have separate citations for each chapter where only the |chapter= and |chapterurl= parameters differ:
Boghog (talk) 18:47, 21 April 2015 (UTC)
My first reaction to your 'appended links' idea was that we shouldn't create our own linked pseudo-TOC given the publisher's apparent desire not to have a linked TOC hosted by the organization they actually licensed the content to. But all the other ideas do essentially the same thing, so that's a bit silly. I think I like that idea in combination with {{rp}} chapter labels best, as it's least intrusive in the text, makes clear how many citations go to a general reference, and doesn't require a separate list or potentially fragile formatting. Opabinia regalis (talk) 20:49, 21 April 2015 (UTC)

───────────────────────── I've not done much non-standard reference citation so I'll wait until you've done a couple so that I can see the format in context before doing any more. The ones I added yesterday shouldn't be too difficult to reformat. T.Shafee(Evo﹠Evo)talk 12:24, 22 April 2015 (UTC)

You're the one currently doing the work, so I think that means you get to decide :) Opabinia regalis (talk) 19:01, 22 April 2015 (UTC)

MBOC references[edit]

Article

Genes[1]:2 are numerous[1]:4 and useful[1]:4.1

References

  1. ^ a b c Alberts B, Johnson A, Lewis J, Raff M, Roberts K, Walter P (2002). Molecular Biology of the Cell (Fourth ed.). New York: Garland Science. ISBN 978-0-8153-3218-3.

Glossary
Ch 2: Cell Chemistry and Biosynthesis
2.1: The Chemical Components of a Cell
Ch 4: DNA and Chromosomes
4.1: The Structure and Function of DNA
4.2: Chromosomal DNA and Its Packaging in the Chromatin Fiber
Ch 6: How Cells Read the Genome: From DNA to Protein
6.1: DNA to RNA
6.2: RNA to Protein
Ch 7: Control of Gene Expression

So {{rp}} labels the chapter number but does not provide any easy link to the actual information. Therefore it's combined with a list of chapter links. the benefit is that the {{rp}} template is relatively easy to maintain and the list of chapter links doesn't require maintainance and places all the MBOC links together. As stated above, there's basically no way to avoid linking individually to chapters if we want to cite MBOC. I'll finish building the chapter list over the next couple of days. T.Shafee(Evo﹠Evo)talk 01:29, 27 April 2015 (UTC)

I've finished adding MBOC references up to section 3 (gene expression). Also, whoever originally wrote the gene expression section of the article really liked semicolons! T.Shafee(Evo﹠Evo)talk 10:51, 27 April 2015 (UTC)
Looks great, I like the collapsible box! I can't find it at the moment, though - IIRC there is somewhere an agreement not to use collapsed boxes for references for accessibility reasons. I don't see it in WP:ACCESSIBILITY so I could be misremembering, and since the box contains links and not the reference note itself, it's probably fine. Just wanted to mention it in case someone recognized the issue. Opabinia regalis (talk) 07:50, 28 April 2015 (UTC)
@Opabinia regalis and Evolution and evolvability: The guideline is MOS:COLLAPSE, which states "...boxes that toggle text display between hide and show, should not conceal article content, including reference lists ... When scrolling lists or collapsible content are used, take care that the content will still be accessible on devices that do not support JavaScript or CSS." I checked this article on my phone, a mid-2011 model, and that entire box just doesn't appear at all using the default mobile view. I tried setting the template parameter expand=true so the box is expanded by default but that made no difference. Maybe better to change to a bulleted or indented list? Adrian J. Hunter(talkcontribs) 10:50, 30 June 2015 (UTC)
@Adrian J. Hunter: Well spotted - It's really irritating when templates don't work properly on mobiles! I've changed the MBOC list to be wrapped in {{Hidden begin}} + {{Hidden end}}, which renders properly on phones (default expanded). T.Shafee(Evo﹠Evo)talk 12:31, 30 June 2015 (UTC)
Yep, that works – thanks! Adrian J. Hunter(talkcontribs) 13:23, 30 June 2015 (UTC)

Third vs. Fourth Generation Sequencing[edit]

Nanopore sequencing is described as 4th generation [1] and 3rd generation [2] in Wikipedia. Please review and revise. Definitions of third and fourth generation differ amongst sources. Consider adding a page to describe 4th generation. One distinction is that 3rd is all about very long reads whereas 4th is about in situ (single cell) reads.

Facto Post – Issue 2 – 13 July 2017[edit]

Facto Post – Issue 2 – 13 July 2017
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Editorial: Core models and topics[edit]

Wikimedians interest themselves in everything under the sun — and then some. Discussion on "core topics" may, oddly, be a fringe activity, and was popular here a decade ago.

The situation on Wikidata today does resemble the halcyon days of 2006 of the English Wikipedia. The growth is there, and the reliability and stylistic issues are not yet pressing in on the project. Its Berlin conference at the end of October will have five years of achievement to celebrate. Think Wikimania Frankfurt 2005.

Progress must be made, however, on referencing "core facts". This has two parts: replacing "imported from Wikipedia" in referencing by external authorities; and picking out statements, such as dates and family relationships, that must not only be reliable but be seen to be reliable.

In addition, there are many properties on Wikidata lacking a clear data model. An emerging consensus may push to the front key sourcing and biomedical properties as requiring urgent attention. Wikidata's "manual of style" is currently distributed over thousands of discussions. To make it coalesce, work on such a core is needed.

Links[edit]


Editor Charles Matthews. Please leave feedback for him.

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WikiProject X Newsletter • Issue 13[edit]

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Newsletter • December 2018

This month: A general update.

The current status of the project is as follows:

  • Progress of the project has been generally delayed since September due to development issues (more bitrot than expected, some of the code just being genuinely confusing, etc) and personal injury (I suffered a concussion in October and was out of commission for almost two months as a result).
  • I currently expect to be putting out a proper call for CollaborationKit pilots in January/February, with estimated deployment in February/March if things don't go horribly wrong (they will, though, don't worry). As a part of that, I will properly update the page and send out announcement and reach out to all projects already signed up as pilots for WikiProject X in general, at which point those (still) interested can volunteer specifically to test the CollaborationKit extension.
    • Wikipedia:WikiProject X/Pilots was originally created for the first WikiProject X prototype, and given this is where the project has since gone, it's only logical to continue to use it. While I haven't yet updated the page to properly reflect this:
    • If you want to add your project to this page now, feel free. Just bear in mind that more information what to actually expect will be added later/included in the announcement, because by then I will have a much better idea myself.
  • Until then, you can find me in my corner working on making the CollaborationKit code do what we want and not just what we told it, per the workboard.

Until next time,

-— Isarra 22:44, 20 December 2018 (UTC)

Facto Post – Issue 19 – 27 December 2018[edit]

Facto Post – Issue 19 – 27 December 2018
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Learning from Zotero

Zotero is free software for reference management by the Center for History and New Media: see Wikipedia:Citing sources with Zotero. It is also an active user community, and has broad-based language support.

Zotero logo

Besides the handiness of Zotero's warehousing of personal citation collections, the Zotero translator underlies the citoid service, at work behind the VisualEditor. Metadata from Wikidata can be imported into Zotero; and in the other direction the zotkat tool from the University of Mannheim allows Zotero bibliographies to be exported to Wikidata, by item creation. With an extra feature to add statements, that route could lead to much development of the focus list (P5008) tagging on Wikidata, by WikiProjects.

Zotero demo video

There is also a large-scale encyclopedic dimension here. The construction of Zotero translators is one facet of Web scraping that has a strong community and open source basis. In that it resembles the less formal mix'n'match import community, and growing networks around other approaches that can integrate datasets into Wikidata, such as the use of OpenRefine.

Looking ahead, the thirtieth birthday of the World Wide Web falls in 2019, and yet the ambition to make webpages routinely readable by machines can still seem an ever-retreating mirage. Wikidata should not only be helping Wikimedia integrate its projects, an ongoing process represented by Structured Data on Commons and lexemes. It should also be acting as a catalyst to bring scraping in from the cold, with institutional strengths as well as resourceful code.

Links

Diversitech, the latest ContentMine grant application to the Wikimedia Foundation, is in its community review stage until January 2.

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MediaWiki message delivery (talk) 19:08, 27 December 2018 (UTC)

Request to move over "L."[edit]

At Talk:L. Inc.#Requested move 5 January 2019 there is a proposal that the redirect L. ( → Carl Linnaeus ) be replaced with the article at L. Inc.. Members of this project may be interested. 92.249.211.146 (talk) 04:27, 6 January 2019 (UTC)

Twin needs work[edit]

  • See in particular Talk: Twin# Regarding section "Types of twins and zygosity".
  • When you type "Twin" in the "search Wp" field and click the magnifying glass icon, this article tops the list, as it should, but with the note
    one of two offspring produced in the same pregnancy. Use with P31 on items for one twin
The part I've bolded surely should not be visible there.

--Thnidu (talk) 08:50, 15 January 2019 (UTC)

Invasive species?[edit]

Hi, WikiProject Biology,

I do a lot of work with categories and right now we are seeing many categories involving "invasive species" that are empty. Is there a recategorization going on or deletion of articles involving invasive species? Right now there are 14 invasive categories that have been tagged for deletion as empty categories (see Category:Empty categories awaiting deletion) and I see more coming my way. Because some categories are emptied out of process, categories sit in the empty category for 7 days before they are deleted.

Typically empty categories appear randomly about different topics and this happens when 1) a category has only one article and that article gets deleted or 2) recategorization occurs and a new category system replaces an older one or there is renaming going on. It's unusual to have 14 categories on one subject to appear unless it's an intention editing project. So, I thought I'd post here in case anything funny is going on because I hope members of WikiProject Biology would know about this.

Thanks. Liz Read! Talk! 02:11, 17 January 2019 (UTC)

Natural history of California by region[edit]

Please contribute to this deletion discussion about Category:Natural history of California by region and its subcategories. Marcocapelle (talk) 07:25, 30 January 2019 (UTC)

Facto Post – Issue 20 – 31 January 2019[edit]

Facto Post – Issue 20 – 31 January 2019
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Everything flows (and certainly data does)

Recently Jimmy Wales has made the point that computer home assistants take much of their data from Wikipedia, one way or another. So as well as getting Spotify to play Frosty the Snowman for you, they may be able to answer the question "is the Pope Catholic?" Possibly by asking for disambiguation (Coptic?).

Amazon Echo device using the Amazon Alexa service in voice search showdown with the Google rival on an Android phone

Headlines about data breaches are now familiar, but the unannounced circulation of information raises other issues. One of those is Gresham's law stated as "bad data drives out good". Wikipedia and now Wikidata have been criticised on related grounds: what if their content, unattributed, is taken to have a higher standing than Wikimedians themselves would grant it? See Wikiquote on a misattribution to Bismarck for the usual quip about "law and sausages", and why one shouldn't watch them in the making.

Wikipedia has now turned 18, so should act like as adult, as well as being treated like one. The Web itself turns 30 some time between March and November this year, per Tim Berners-Lee. If the Knowledge Graph by Google exemplifies Heraclitean Web technology gaining authority, contra GIGO, Wikimedians still have a role in its critique. But not just with the teenage skill of detecting phoniness.

There is more to beating Gresham than exposing the factoid and urban myth, where WP:V does do a great job. Placeholders must be detected, and working with Wikidata is a good way to understand how having one statement as data can blind us to replacing it by a more accurate one. An example that is important to open access is that, firstly, the term itself needs considerable unpacking, because just being able to read material online is a poor relation of "open"; and secondly, trying to get Creative Commons license information into Wikidata shows up issues with classes of license (such as CC-BY) standing for the actual license in major repositories. Detailed investigation shows that "everything flows" exacerbates the issue. But Wikidata can solve it.

Links

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MediaWiki message delivery (talk) 10:53, 31 January 2019 (UTC)

Canis lupus arctos[edit]

Is there a reference for what "arctos" means in the naming of Canis lupus arctos ? Does it refer to the thick fur? Is it a pseudo-Classical creation that isn't the Latin word "arctos"? -- 70.51.201.106 (talk) 06:10, 9 February 2019 (UTC)

It's the classical Greek for bear: the Great Bear is a constellation near the North Pole, so the Arctic is the region of the Bear. Chiswick Chap (talk) 08:52, 9 February 2019 (UTC)

Discussion at Wikipedia:Village pump (idea lab)#Attention WikiProjects[edit]

 You are invited to join the discussion at Wikipedia:Village pump (idea lab)#Attention WikiProjects. We are designing a bot script to perform a few article assessment–related tasks and would appreciate your feedback. Qzekrom (talk) 08:52, 23 February 2019 (UTC)

Facto Post – Issue 21 – 28 February 2019[edit]

Facto Post – Issue 21 – 28 February 2019
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The Editor is Charles Matthews, for ContentMine. Please leave feedback for him, on his User talk page.
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What is a systematic review?

Systematic reviews are basic building blocks of evidence-based medicine, surveys of existing literature devoted typically to a definite question that aim to bring out scientific conclusions. They are principled in a way Wikipedians can appreciate, taking a critical view of their sources.

PRISMA flow diagram for a systematic review

Ben Goldacre in 2014 wrote (link below) "[...] : the "information architecture" of evidence based medicine (if you can tolerate such a phrase) is a chaotic, ad hoc, poorly connected ecosystem of legacy projects. In some respects the whole show is still run on paper, like it's the 19th century." Is there a Wikidatan in the house? Wouldn't some machine-readable content that is structured data help?

2011 photograph by Bernard Schittny of the "Legacy Projects" group

Most likely it would, but the arcana of systematic reviews and how they add value would still need formal handling. The PRISMA standard dates from 2009, with an update started in 2018. The concerns there include the corpus of papers used: how selected and filtered? Now that Wikidata has a 20.9 million item bibliography, one can at least pose questions. Each systematic review is a tagging opportunity for a bibliography. Could that tagging be reproduced by a query, in principle? Can it even be second-guessed by a query (i.e. simulated by a protocol which translates into SPARQL)? Homing in on the arcana, do the inclusion and filtering criteria translate into metadata? At some level they must, but are these metadata explicitly expressed in the articles themselves? The answer to that is surely "no" at this point, but can TDM find them? Again "no", right now. Automatic identification doesn't just happen.

Actually these questions lack originality. It should be noted though that WP:MEDRS, the reliable sources guideline used here for health information, hinges on the assumption that the usefully systematic reviews of biomedical literature can be recognised. Its nutshell summary, normally the part of a guideline with the highest density of common sense, allows literature reviews in general validity, but WP:MEDASSESS qualifies that indication heavily. Process wonkery about systematic reviews definitely has merit.

Links

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MediaWiki message delivery (talk) 10:02, 28 February 2019 (UTC)

One of your project's articles has been selected for improvement![edit]

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Hello,
Please note that Organ (anatomy), which is within this project's scope, has been selected as one of Today's articles for improvement. The article was scheduled to appear on Wikipedia's Community portal in the "Today's articles for improvement" section for one week, beginning today. Everyone is encouraged to collaborate to improve the article. Thanks, and happy editing!
Delivered by MusikBot talk 00:05, 18 March 2019 (UTC) on behalf of the TAFI team